Ex vivo human brain volumetry: Validation of MRI measurements.

Purpose: The volume of in vivo human brains is determined with various MRI measurement tools that have not been assessed against a gold standard. The purpose of this study was to validate the MRI brain volumes by scanning ex vivo, in situ specimens, which allows the extraction of the brain after the scan to compare its volume with the gold-standard water displacement method (WDM).

Methods: The 3T MRI T₂-weighted, T₁-weighted, and MP2RAGE images of seven anatomical heads fixed with an alcohol-formaldehyde solution were acquired. The gray and white matter were assessed using two methods: (i) a manual intensity-based threshold segmentation using Display (MINC-ToolKit) and (ii) an automatic deep learning-based segmentation tool (SynthSeg). The brains were extracted and their volumes measured with the WDM after the removal of their meninges and a midsagittal cut. Volumes from all methods were compared with the ground truth (WDM volumes) using a repeated-measures analysis of variance.

Results: Mean brain volumes, in cubic centimeters, were 1111.14 ± 121.78 for WDM, 1020.29 ± 70.01 for manual T₂-weighted, 1056.29 ± 90.54 for automatic T₂-weighted, 1094.69 ± 100.51 for automatic T₁-weighted, 1066.56 ± 96.52 for automatic magnetization-prepared 2 rapid gradient-echo first inversion time, and 1156.18 ± 121.87 for automatic magnetization-prepared 2 rapid gradient-echo second inversion time. All volumetry methods were significantly different (F = 17.874; p < 0.001) from the WDM volumes, except the automatic T₁-weighted volumes.

Conclusion: SynthSeg accurately determined the brain volume in ex vivo, in situ T₁-weighted MRI scans. The results suggested that given the contrast similarity between the ex vivo and in vivo sequences, the brain volumes of clinical studies are most probably sufficiently accurate, with some degree of underestimation depending on the sequence used.